Using recently developed prediction models and performance metrics, we have examined the incremental contribution of 9p21.3 variation to cardiovascular risk among more than 22,000 initially healthy Caucasian participants in the Women's Genome Health Study. Like a previous report examining this same variation among Caucasian men, (20
) we find a strong and significant association of 9p21.3 variation with CVD in Caucasian women. However, in our data, knowledge of this genetic variation only marginally improved the classification of risk prediction in a model based on ATP-III covariates and did not improve classification in a model that included family history and CRP (Reynolds Risk Score covariates). In both settings, the addition of genotype information had no appreciable effect on the c-index
The rs10757274 SNP is one of a cluster of tightly linked SNPs associated with coronary artery disease, (3
) MI, (3
) and stroke, (21
) abdominal aortic aneurysm,(6
) and intracranial aneurysm (6
) at 9p21.3. The linkage disequilibrium block spanning these SNPs extends 28kb from rs10757274 toward the telomere about 55.7kb from the 3’ end of the CDKN2B transcript, although weaker linkage disequilibrium continues through the CDKN2A/CDKN2B gene region. The major transcript of a third gene, MTAP, corresponds with an entirely separate linkage disequilibrium block still further toward the telomere, but an alternatively spliced variant may be transcribed into the linkage disequilibrium block containing CDKN2A/CDKN2B. Toward the centromere, the linkage disequilibrium block including the associations with the arterial diseases extends 28.3kb bases from rs10757274 and is juxtaposed with a smaller linkage disequilibrium block of about 6.9kb including a SNP associated with diabetes (rs10822661).(6
While the mechanism of the association between the rs10757274 genotype and CVD remains unclear, the magnitude of association observed in our study of women is consistent with previously reported associations for 9p21.3 SNPs in studies largely comprised of men.(5
) Our data also extend prior work demonstrating significant association with incident stroke.(21
) As we were unable to find correlations between polymorphisms in rs10757274 and standard lipids, apolipoprotein B 100, apolipoprotein A-I, lipoprotein(a), or hsCRP, our data provide further evidence that the effect of this genetic variation is unlikely to reflect genetic differences in lipid levels or biomarkers of hemostasis and inflammation.
Despite high prevalence of the risk allele and consistent association of rs10757274 with vascular events, inclusion of genotype information did not lead to any substantive improvement in global risk prediction in our study. Instead, the addition of genotype information to a model which included CRP and family history of CVD actually worsened classification. Thus, while knowledge of variation in chromosome 9p21.3 may yield important pathophysiologic insights into atherothrombosis, it appears unlikely that screening for SNPs in this region will have clinical utility for daily practice.
Improved cardiovascular risk prediction has clear potential for public health, but has been difficult to achieve, and the potential role of genetic information is just beginning to be explored. Whether or not a precisely measured gene panel will prove superior to knowledge of family history of CVD is uncertain, though combination scores have had promising effects on prediction.(2
) As shown in this paper, and as expected from statistical work by Pepe (22
) and Cook,(17
) single polymorphisms alone, even common ones with consistent modest associations, are unlikely to improve prediction.
Our study benefits from a large sample size and extensive prospective follow-up. However, because of the small numbers of non-Caucasian participants, our results are limited to Caucasian women. Further studies are needed in other populations, both of the association between the rs10757274 genotype and CVD and the resultant effect on risk prediction. Our study also evaluated only variation at chromosome 9p21.3 and thus does not exclude the possibility that multigene panels might result in larger proportions of individuals reclassified correctly. Our study did not examine the additional effect of genotype relative to the previously published risk scores, but rather examined the additional effect after refitting all covariates in the same population. While this comparison potentially limits the generalizability of our results, it preserves their validity.
In conclusion, we confirmed the association of 9p21.3 with total CVD as well as coronary heart disease, MI and stroke in a large prospective cohort of Caucasian women. However, addition of the 9p21.3 genetic variation did not improve discrimination or classification of predicted risk achieved with traditional risk factors, CRP and family history of CVD.